Darkest before dawn
by WildLillys
Summary: This is a human AU. It will contain lots of fluff(once I'm done with introductions) and bonding! Some things are different than the original, but hey, that's what fanfics are for!
1. chapter 1

Long ago in Japan, there existed a ninja clan known as the foot. It was a well known peaceful organization.

Among the Foot's ranks was Hamato Yoshi, he was a man at the peak of his life, he was a great ninja warrior and was known for his wise mind and intelligence.

But there was another man, who was as well known as Yoshi, his name was Oroku Saki, his skills were at the same level as yoshi but he was known for his ruthless and merciless nature with his enemies.

The two were like rivals most of the time and despite saki's constant disapproval of yoshi's gentle ways, they were good friends.

Until they met Tang Shen. She was a beautiful women with hair as black as the night sky. Her eyes always shone with mirth.

Hamato Yoshi often clashed Oroku saki over the love of Tang Shen. They're rough friendship all but vanished.

When it became clear that Tang Shen loved only Yoshi, saki arrived at her home and started a fire there, thinking that if he can't have her then no one will, especially not yoshi.

Both of the friends turned enemies faced off against each other in the fire, though they were equally skilled. However, with a stroke of luck on yoshi's side, he managed to pushed saki back and leave to search for his lover but Tang Shen perished in the fire, leaving behind a heartbroken and devastated yoshi.

Yoshi then, in an attempt to smother the agony of loss, decided to go to New York city. There he founded a small martial arts school -just like Tang Shen wanted- that quickly gained fame and credit. For now everything was fine.

While all of that happened in New York, back in Japan, Oroku Saki continued to train so he can become stronger so he can extract his revenge on yoshi. He was fueled by a thirst for vengeance for both taking away Tang Shen and for disfiguring his face forcing saki to hide behind a metal helmet.

Saki eventually became high-ranking member of the organization, and was tasked with leading a branch of the Foot in New York aiding his objective of revenge. Once there, Saki adopted the mantel of the shredder and led the clan to the highest ranks of the underworld, specializing in burglary, espionage, and assassination. Yet the entire time, Saki sought the opportunity to slay Hamato Yoshi.

One night Yoshi returned home to find his apartment ransacked. Yoshi then saw the Shredder, who revealed his identity as Oroku Saki.

To say that yoshi was shocked would be an understatement. Saki launched his attack on yoshi with all of his pent up hatred. They both engaged in a fight that made saki aware of the difference in strength between the two.

That only made him angrier, his hatred growing into despise. He was weaker than yoshi, and after all of his training. So in order to save his life, knowing that yoshi wouldn't hesitate to kill him this time, he targeted yoshi's emotional wound that was still fresh in both of their minds despite the time that had passed.

In the end yoshi abandoned his house and ran away from the scene as saki did the same.

Yoshi's fear of being hunted like a measly prey by saki got the better of him as his panicked and frightened brain decided to hide in the sewers at least for now.

Around the area of the manhole that yoshi used to entre the sewers, a blind man was crossing the road when a truck labeled "T.C.R.I" almost ran him down. A young man ran out to save the blind man, the two random citizens were safe. But as the truck swerved, the back doors flew open. A container of glowing green goo fell out and was subsequently washed down the drain...

...Down the drain and directly at the place of where yoshi had ventured through the sewers and the jar of goo crashed beside him, coating him with its viscous contents.

Yoshi immediately tried brushing the green goo off of him as fast as possible as he knew that it might cause him some damage (It was quite obvious from its appearance alone)

However he wasn't fast enough. The green contents had already taken effect on him.

It was a painful procedure, he could feel his bones shifting, his muscles contracting and relaxing at a fast pace. But the pain was more intense in his lower back and his skull.

By the time it was over, he was gasping for breath as he laid on the cold concrete floor of the sewers.

His vision was blurry but he could clearly see his -now- four fingered furry grey hand. It had taken him a full ten minutes for the shock to wear off. Though he couldn't stop himself from twitching when he saw his tail.

Yoshi searched for a clean enough pipe that could show his reflection, only to be greeted by a face of a huge rat, black eyes staring back at him.

'I'm a rat now. A huge mutated rat. Great.' He thought sarcastically. He suddenly felt very tired. All the adrenaline that had been previously pumping in him had faded from his system, leaving him worn out.

He sagged his shoulders and decided to search for a place to spend the night. He deduced that it was best to stay hidden in here for now, who knows what would the world do to a giant, talking, intelligent rat roaming around.

They would probably want to dissect him 'in the name of science'. He felt a shudder go through him at that thought. Just thinking about it gives him goosebumps.

He doesn't want that to happen to him, i mean, who would? Hopefully whatever that substance did to him, it would be only temporary.

This is all so very troublesome. It was overly infuriating!! He sure hopes that all this misfortune would end soon.

But for some reason he felt that things would only get complicated from here on out...


	2. chapter 2

The night sky had never looked as enchanting as it was at the moment. The tiny shining dots that are the stars. Scattered throughout the sky. Like pearls. The stars were illuminating the black void beautifully. There were waves of navy blue bleeding into the blackness.

The scene was that of enchanting tranquility.

The moon, bright silver, complementing the stars in the stillness of the night.

The shadows danced mirthfully across the buildings of the insomniac city.

The lights from different shops and vehicles were but mere glimmering blurs of reds and oranges.

Things seemed normal. It was the same routine every other night. It seemed peaceful enough.

But things aren't always as they seem...

In one of New York's buildings that the leader of the criminal organization known as the foot clan, the shredder, used as his hideout, things were eerily quiet.

In one of the building's many vile laboratories, lay four infants, each on a metal table.

They were unnaturally still as they are currently in a drug induced sleep. If they had been awake they would have been wailing in fear. The cold surface of which they lay on wouldn't have helped in the slightest.

Those four infants are just orphans. Orphans that have been kidnapped from the orphanage. The shredder wanted some guinea pigs to test the effects of the newest chemical, which he obtained from an acquaintance.

The chemical itself was intriguing, after a lot of experimenting, they discovered that it can cause different effects, mutations, depending on the test subjects.

For example, it can cause the test subject to become an animal hybrid, depending on the last animal the subject came in contact with.

But other times it can cause melting of flesh or damage to the system, causing horrible disfiguring to the subject.

In short, it changes the genetic structure of all organisms that come into contact with it.

The shredder became even more interested in that ooze. He wanted to experiment more, but he had no more test subjects, so he decided to get some.

He ordered his foot soldiers to kidnap some orphans, preferably young ones, so that they cause less trouble as they can be controlled easily.

From then, every week, he would get new test subjects ranging around a dozen or so. He doesn't care about the panic that he caused in the city and within the authorities. All he needs are test subjects.

But most of those little test subjects, ended up dead. The ooze has put too much stress on their bodies, resulting in immediate death.

During each experiment, the subject would be chained to a metal table were scientists would be able to study the effect of the ooze.

They didn't want any trouble with crying children so, they would be subdued before any experimenting took place. But those who were put under, died during the test.

In the end, they decided to keep them awake while the testing was going on.

The children, ranging from few months to four years old, would be chained to the same table on which the previous test subject lost their life.

The moment the ooze touches their skin, the horrible searing pain spreads through their bodies as they scream and wail with their raw throats, begging for mercy, thrashing around, kicking wlidley as they try to escape.

But the scientists wouldn't care, they would stare emotionlesslly at the souls having around a year of their lives.

While three quarters of the subjects die due to the sheer pain, the remaining quarter would survive, though later they would wish they didn't.

The mutated survivors would later be brought for dissection. They would try fruitlessly to escape. But they would be chained to the same damned table from before.

They would watch helplessly in pain while the scientists hovered over them, with a scalpel in hand of each.

They could feel each touch of their fingers, each prob of their sharp tools and each snip of their scissors.

Examining each part of their now mutated organs, writing down their observations. It was atrocious, heinous!

But those survivors don't last long either. Due to the continuous experimenting and not getting proper nutrition, they lose their short lives in their confinements.

Shredder decided to try something new with the remaining four test subjects.

So, instead of covering them from head to toe with the ooze, they started injecting small amounts of the gooy chemical into their bloodstreams. They could even drug them as it wouldn't kill them, avoiding ear damage.

The four infants where surrounded by scientists from all sides, they were getting ready to inject the fifth shot into them. They had decided to give them a shot every six hours so the blood and the chemical can fuse together.

The problem is that after getting the second shot, the infants started having a bad fever. But the scientists didn't give them medication, they didn't want to hinder the fusion, and if they died from over heating, then too bad.

They also realised that this shot could very well kill the immobilized infants. But it's all in the name of science.

Just a small prick and the four would follow all the other 50 to 55 infants that died here during the last few months.

Slowly, the needle inched closer to the skin of the oldest child, the one with raven hair.

Slowly, ever so slowly, the sharp silvery needle was a few centimeters away from the boy's skin.

Suddenly, the double door of the laboratory burst open, and there stood a large, grey furred, rat in all of his glory.

He wore a light brown robe with a dark brown belt wrapped around his middle.

All the scientists halted whatever it is that they were doing to stare at the rat. Their thoughts left the four infants and concentrated on the intruder, wanting to experiment on him.

The mutated Yoshi saw the scientists' eager expression and decided that it was the best time to attack.

He leaped over the first scientist and kicked the next in the face, still airborne, landing on the ground, he twisted his body as he swiped the legs of the scientists that surrounded him.

To be honest with himself Yoshi was actually feeling a little smug, but only a little.

It hadn't taken long before yoshi finished the last of them. He turned his body to face the remaining four innocent souls.

He carefully collected all the four into his arms and was thoughtful enough to grab the four's files, hoping that it contained some sort of information about the infants.

He made his way outside the building fast, without making any sound, just like he had entered. And it's more likely that no one will know what had happened in that room until one of the scientists wakes up.

When he was at a safe distance from the building he allowed himself to relax a little as he trudged to his new home in the sewers.

Once inside, he gently laid the four on a blanket that he found and proceeded to cool their burning foreheads.

While doing so, he recalled what he heard during one of his trips to the topside for food. He had been hiding in the shadows when he heard the telltale sounds of footsteps of amateur ninjas.

Blending into the shadows he saw as the ninjas stopped in front of him, recognising the uniform of the foot clan, he listened carefully as the two careless ninjas practically split all of the foot clans' secrets.

He found out a lot of things, like how the new recruits are trained, their missions, latest assassinations and all that.

He also found out that the shredder, because he wasn't saki anymore, had been kidnapping orphan infants for his own sick satisfaction of experimentation.

Yoshi was about ready to pounce on the amateurs and demand they tell him the place of their hideout, but decided against it as it would draw the shredder's attention.

So instead he followed the soldiers, because they aren't ninjas that's for sure, as they made their way back to the foot clan's hideout. Planning to rescue the poor souls in there.

Really though, Yoshi hadn't thought of what was he supposed to do with them, now that they were saved.

He can't return them to the orphanage, as shredder would get them again, but this wasn't the best living conditions for infants.

Oh well, guess he'll have to double his efforts while searching for food, it seems that he will have four new additions.

Four new sons . . .


	3. chapter 3

It wasn't supposed to be that way. He wasn't supposed to have four sons. But he does. And that wasn't supposed to happen.

But then again, he wasn't supposed to mutate into a giant rat and live in the sewers, either, now was he? No, he wasn't.

So, yoshi had to take care of four orphan infants. And mind you, he has no knowledge of how to do such a thing, no experience whatsoever.

The fever of the four innocent souls had broke by the end of the next three days, and two out of four caused the most trouble, really, it's either they are fighting each other or causing trouble individually somewhere across their new home.

He then realised that he can't continue referring to them as infants, so he sat down infront of the four, who regarded him with curious wide eyes.

"What to name you...?" he mumbled softly to himself, not expecting an answer from any of the infants.

A thought crossed his mind. It was a memory of Tang Shen. A memory of when she introduced him to renaissance art.

He spent a small moment reminiscing about the past, but snapped out of if soon.

He then placed a hand on the head of the shining honey eyed, raven haired boy "your name will be Leonardo" he said with a small smile.

His hand travelled towards infant with sparkling baby blue eyes and blond hair "and yours will be... Michelangelo" his smile widening a bit.

He turned towards the soft mahogany eyed brunet, placing his hand on the boy's head he said "you will be... Donatello"

Yoshi glanced at the last boy, he reached out towards the stubborn green eyed, ginger haired boy "and you will be Raphael"

The new addition to yoshi's family started giggling and clapping their hands, soft laughs erupted from the four, cheering the gloomy atmosphere of the sewers.

To yoshi, it seemed as if they understood what happened. He grinned in happiness. Who would have thought his life would take such a drastic change?

 **Small time skip**

Yoshi sat in one corner with a book that he managed to salvage in hand, he glanced at the files that lay across the concrete floor. He still haven't read them and now that his sons, especially the two troublemakers, are asleep, it was the best time to read them.

The rodent reached a hand towards the first file, and coincidentally it was the oldest's file, Leonardo.

He opened it and scanned the information, trying to find anything useful.

Name: unknown

Sex: male

Date of birth: 11th August 20XX

Current age: 3 years

Distinct physical features: black hair, orange eyes, average weight, average height.

Parents: unknown

Date of admission to the orphanage: 4th March 20XX

Medical conditions: none

The mutated rodent wasn't sure if that was useful or not. On one hand, he couldn't find anything out about their parents.

But on the other hand, he found other useful information, like his blood type, age and birthday. Thankfully Leonardo isn't suffering from any medical condition.

Now seeing that the advantages, quite obviously, outnumbered the disadvantages, and feeling quite stupid at the doubt, he continued with his self appointed task.

He reached for the next file, it was Michelangelo's file.

Name: unknown

Sex: male

Date of birth: 1st March 20XX

Current age: 1 year

Distinct physical features: blond hair, blue eyes, below average weight, below average height.

Parents: unknown

Date of admission to the orphanage: 4th March 20XX

medical conditions: none

His blond son was 1 year old? He looks younger than that... almost 3 months or so.

Well he is underweight, he'll have to take care of that.

Yoshi reached for the third file

Name: unknown

Sex: male

Date of birth: 21st September 20XX

Current age: 2 year

Distinct physical features: ginger hair, green eyes, average weight, average height.

Parents: unknown

Date of admission to the orphanage: 4th March 20XX

medical conditions: none

Ah, it was Raphael's. Two years old, eh? That makes Leonardo the oldest of the bunch.

For some reason yoshi feels this won't appeal to his ginger headed son.

He shook his head to rid himself of those thoughts, which, hopefully, won't happen and reached a hand towards the last file, which more than likely is Donatello's.

Name: unknown

Sex: male

Date of birth: 13th February 20XX

Current age: 1 year

Distinct physical features: brown hair, brown eyes, below average weight, below average height.

Parents: unknown

Date of admission to the orphanage: 4th March 20XX

medical conditions: Born with a weak immune system. Has sickle cell anemia

Oh my, a weak immune system? And anemia on top of that...

Yoshi sighed in sympathy. The poor soul. But he will have to at least try and find some kind of cure. But it isn't the easiest considering their living conditions...

The rodent closed the file and leaned back on the wall behind him. His gaze landed on his four sons.

Leonardo is the oldest. Then comes Raphael, younger by a year. Then there is Donatello and Michelangelo. Those two are the tiniest of the four, they almost look like twins.

But considering the fact that, despite both being 1 year old, Donatello is born before Michelangelo by 15 days, so he's older than the blond.

There is a year difference between Leonardo and Raphael, a year difference between Raphael and Donatello Michelangelo.

But only 15 days difference between his two youngest sons.

Both Leonardo and Raphael should be able to speak, or at least say a few words. But they aren't. They can understand his words but are apparently unable to talk.

It seems that their previous living conditions weren't the best. It looks like they were not around people often whom the two can learn words from.

Oh well, now he can enjoy the pleasure of hearing their first words, which is a memorable moment for every parent!

But the thing is... they are from the same orphanage. That's not weird in itself but the fact that the dates when they were admitted to the orphanage, for all four of them, is the same.

Is this some kind of freaky coincidence? On the same day? And those four end up here... Could their parents be linked?

The rodent sighed and decided not to dwell on it anymore. All that matters is that those four are now his sons. His adorable precious sons.


End file.
